Over 150 million people are infected with hepatitis C virus (HCV) worldwide. Current standard of care (SOC) based on the foundation of pegylated alpha interferon is inadequate for many patients and associated with significant side effects. A better understanding of the molecular virology of HCV can lead to better rational design for newer and more effective therapies. So far, viral proteins have been the predominant focus of therapeutic targets. However, research has shown that the HCV RNA itself plays many important roles in the viral life cycle, beyond information storage. Specifically, the 5' untranslated region (UTR) of the HCV RNA and the corresponding region on the complementary negative strand, called the 3' term (-) - which is the site for initiation of progeny plus strand genomes - contain distinct RNA elements that are important for their regulatory functions. Using a novel RNA secondary structure mapping tool named sf-SHAPE (single fluorophore selective 2'-hydroxyl acylation analyzed by primer extension), I have determined the secondary structure of the HCV 5' UTR and have also shown that the 5' UTR secondary structure is altered by the presence of the miR-122, an abundant, liver-specific, micro RNA that has been shown to be required for HCV replication. However, much less is known about the structural details of the 3' term (-) and how they relate to this region's critical functions in th virus's life cycle. Since sf-SHAPE allows for rapid and accurate determination of RNA secondary structures, I propose here to study the RNA secondary structure of the HCV 3' term (-) in multiple biological contexts. Such information is critical to a better understanding of the HCV lif cycle, in aiding the rational design of potential next-generation anti-HCV therapies, and for future screening for inhibitors that might purposefully target essential RNA elements in the 3' term (-), thereby providing proof- of-concept for a potential novel class of RNA-targeting small molecules with application to HCV and RNA viruses in general.